improved bimaculatus data; example of plotting long taxon names

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
-Version: 2.16-5
-Date: 2021-05-06
+Version: 2.16-7
+Date: 2021-05-09
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu"),
 	  person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <kingaa@umich.edu>

R/anolis.R

@@ -8,9 +8,9 @@
 #' Size dimorphism was calcuated as the log-ratio of male snout-to-vent length to female snout-to-vent length (males are larger).
 #' 
 #' In this example, we tested three models of evolution:
-#' Brownian motion, Ornstein-Uhlenbeck with one global optimum, and Ornstein-Uhlenbeck with 7 optima (one for each ecomorph type plus an additional one for an "unknown" type).
+#' Brownian motion, Ornstein-Uhlenbeck with one global optimum, and Ornstein-Uhlenbeck with seven optima (one for each ecomorph type plus an additional one for an "unknown" type).
 #' 
-#' For the 7-optima model, we assigned each terminal branch to an optimum according to the ecomorph type of the extant species.
+#' For the seven-optima model, we assigned each terminal branch to an optimum according to the ecomorph type of the extant species.
 #' Because we had no information to help guide hypotheses about internal branches, we assigned
 #' internal branches to the "unknown" selective regime.
 #' The phylogeny of these species is consistent with and adaptive radiation, with a burst of speciation events early in the evolutionary history of this clade (see phylogeny in Butler & King (2004) or example below).
@@ -24,7 +24,7 @@
 #'   - `node`: Labels for the nodes.
 #'   - `species`: Names of extant species.
 #'   - `log.SSD`: Log sexual size dimorphism of extant species.
-#'   - `ancestor`: Ancestor node.
+#'   - `ancestor`: Name of ancestor node.
 #'   - `time`: Time of node.
 #'   - `OU.1`: a factor with one level, `ns`.
 #'   - `OU.7`: a factor with levels corresponding to ecomorph (`tg`, `tc`, `gb`, `cg`, `tw`, `tr`, `anc`).

R/bimac.R

@@ -5,7 +5,7 @@
 #' The data frame has the following columns:
 #' `species` which are species names,
 #' `size` which is the phenotypic data,
-#' and the variables `ancestor` and `time` which specify the topology of the phylogeny and the location of the nodes in time, respectively.
+#' and the variables `node`, `ancestor`, and `time` which specify the topology of the phylogeny and the location of the nodes in time, respectively.
 #' The columns `OU.1`, `OU.3`, `OU.4`, and `OU.LP` specify four hypothetical arrangements of selective regimes.
 #' Explanations of the data follow:
 #' \describe{
@@ -14,31 +14,36 @@
 #'     In this group of lizards, head length correlates very strongly with snout-to-vent length and the cube root of mass, which are standard measures of body size.
 #'     The data are head lengths in mm; note that we use the log of this value in analyses.
 #'   }
-#'   \item{Tree topology}{
-#'     The tree topology is encoded via two vectors: `ancestor` and `time`.
-#'     Each node of the' phylogenetic tree has a corresponding row in the data frame, numbered from 1 to 45.
-#'     The columns `ancestor` and `time` specify the phylogeny.
-#'     The `ancestor` variable specifies the topology: it is a list indicating the ancestor of each node.
-#'     The root node has ancestor 0.
-#'     The variable `time` specifies the temporal location of each node, with the root node being at time 0.
+#'   \item{Tree structure}{
+#'     The phylogenetic tree is encoded via three variables:
+#'     `node`, `ancestor`, and `time`.
+#'     The `node` variable gives a name to each node.
+#'     The `ancestor` variable names the ancestor of each node.
+#'     The root node has no ancestor (i.e., \code{ancestor=NA}).
+#'     The variable `time` specifies the temporal location of each node, the root node being at time 0.
 #'   }
 #'   \item{Specifications of selective regimes.}{
 #'     (Columns `OU.1`, `OU.3`, `OU.4`, `OU.LP`).
-#'     These columns are factors, the levels of which correspond to the "paintings" of the respective adaptive regime hypotheses onto the phylogeny (see [paint()]).
+#'     These columns are factors, the levels of which correspond to the \dQuote{paintings} of the respective adaptive regime hypotheses onto the phylogeny (see [paint()]).
 #'     Each selective regime is named (small, medium, large, etc.).
 #'     Each column corresponds to a different painting of the selective regimes, and thus to a different hypothesis.
 #'     In this example, there are 3 alternative models (see Butler & King 2004): `OU.4` is 4-regime model, `OU.3` is 3-regime model (all ancestors are medium), `OU.LP` is the linear parsimony model.
 #'   }
+#'   \item{Other variables}{
+#'     In addition to the above, there is a two-letter code for each taxon (`spcode`) and the name of the island on which the taxon is found (`island`).
+#'   }
 #' }
 #' 
 #' @name bimac
 #' @rdname bimac
 #' @docType data
 #' @family examples
-#' @format A data frame with 45 observations on the following 8 variables.
+#' @format A data frame with 45 observations on the following 11 variables.
 #' \describe{
 #'   \item{node}{Labels for the nodes.}
+#'   \item{spcode}{Two-letter code for each taxon.}
 #'   \item{species}{Species names for extant species.}
+#'   \item{island}{Name of the island on which the population is found.}
 #'   \item{size}{Body size (head length in mm) of extant species.}
 #'   \item{ancestor}{Ancestral node.}
 #'   \item{time}{Time of node.}

R/plot.R

@@ -17,7 +17,7 @@
 #' There must be at least as many colors as levels in the `regimes`.
 #' @param labels character; taxon labels.
 #' @param margin numeric; width of the right margin (as a fraction of the plot width).
-#' Adjust this if labels are clipped.
+#' Adjust this if labels are clipped (see Examples below).
 #' @param text_opts options for the labels; passed to [`text`][graphics::text()].
 #' @param legend_opts options for the the legend; passed to [`legend`][graphics::legend()].
 #' @param ... additional arguments, passed to [`plot`][graphics::plot()].
@@ -47,7 +47,7 @@ tree.plot.internal <- function (
   rx <- range(x@times,na.rm=T)
   margin <- as.numeric(margin)
   if (!(length(margin)==1 && isTRUE(margin>=0 && margin<1)))
-    pStop("plot",sQuote("margin")," should be between 0 and 1.")
+    pStop("plot",sQuote("margin")," should be one number between 0 and 1.")
   rxd <- margin*diff(rx)/(1-margin)
   anc <- x@anc.numbers
   root <- which(is.root.node(anc))

data/bimac.csv

@@ -1,46 +1,46 @@
-node;species;size;ancestor;time;OU.1;OU.3;OU.4;OU.LP
-1;NA;NA;NA;0;ns;medium;anc;medium
-2;NA;NA;1;12;ns;medium;anc;medium
-3;NA;NA;2;32;ns;medium;anc;small
-4;NA;NA;3;34;ns;medium;anc;small
-5;NA;NA;4;36;ns;medium;anc;small
-6;NA;NA;3;36;ns;medium;anc;small
-7;NA;NA;1;8;ns;medium;anc;medium
-8;NA;NA;7;13;ns;medium;anc;medium
-9;NA;NA;8;18;ns;medium;anc;large
-10;NA;NA;9;23;ns;medium;anc;large
-11;NA;NA;10;28;ns;medium;anc;large
-12;NA;NA;9;28;ns;medium;anc;large
-13;NA;NA;8;22;ns;medium;anc;medium
-14;NA;NA;13;26;ns;medium;anc;medium
-15;NA;NA;14;34;ns;medium;anc;medium
-16;NA;NA;15;36;ns;medium;anc;medium
-17;NA;NA;7;28;ns;medium;anc;medium
-18;NA;NA;17;30;ns;medium;anc;medium
-19;NA;NA;18;34;ns;medium;anc;medium
-20;NA;NA;19;36;ns;medium;anc;medium
-21;NA;NA;20;37;ns;medium;anc;medium
-22;NA;NA;19;36;ns;medium;anc;medium
-23;po;13.5;2;38;ns;small;small;small
-24;se;14.3;4;38;ns;small;small;small
-25;sc;14.3;5;38;ns;small;small;small
-26;sn;14.2;5;38;ns;small;small;small
-27;wb;14.5;6;38;ns;small;small;small
-28;wa;14.9;6;38;ns;small;small;small
-29;be;23.6;10;38;ns;large;large;large
-30;bn;27.1;11;38;ns;large;large;large
-31;bc;27.9;11;38;ns;large;large;large
-32;lb;28.6;12;38;ns;large;large;large
-33;la;28.8;12;38;ns;large;large;large
-34;nu;21.1;13;38;ns;medium;medium;medium
-35;sa;18.3;14;38;ns;medium;medium;medium
-36;gb;19.7;15;38;ns;medium;medium;medium
-37;ga;18.8;16;38;ns;medium;medium;medium
-38;gm;19.6;16;38;ns;large;large;large
-39;oc;22.3;17;38;ns;medium;medium;medium
-40;fe;28.4;18;38;ns;medium;medium;medium
-41;li;18.7;20;38;ns;medium;medium;medium
-42;mg;18.9;21;38;ns;medium;medium;medium
-43;md;19.9;21;38;ns;medium;medium;medium
-44;t1;21.3;22;38;ns;medium;medium;medium
-45;t2;21.5;22;38;ns;medium;medium;medium
+node;spcode;species;island;size;ancestor;time;OU.1;OU.3;OU.4;OU.LP
+1;NA;NA;NA;NA;NA;0;ns;medium;anc;medium
+2;NA;NA;NA;NA;1;12;ns;medium;anc;medium
+3;NA;NA;NA;NA;2;32;ns;medium;anc;small
+4;NA;NA;NA;NA;3;34;ns;medium;anc;small
+5;NA;NA;NA;NA;4;36;ns;medium;anc;small
+6;NA;NA;NA;NA;3;36;ns;medium;anc;small
+7;NA;NA;NA;NA;1;8;ns;medium;anc;medium
+8;NA;NA;NA;NA;7;13;ns;medium;anc;medium
+9;NA;NA;NA;NA;8;18;ns;medium;anc;large
+10;NA;NA;NA;NA;9;23;ns;medium;anc;large
+11;NA;NA;NA;NA;10;28;ns;medium;anc;large
+12;NA;NA;NA;NA;9;28;ns;medium;anc;large
+13;NA;NA;NA;NA;8;22;ns;medium;anc;medium
+14;NA;NA;NA;NA;13;26;ns;medium;anc;medium
+15;NA;NA;NA;NA;14;34;ns;medium;anc;medium
+16;NA;NA;NA;NA;15;36;ns;medium;anc;medium
+17;NA;NA;NA;NA;7;28;ns;medium;anc;medium
+18;NA;NA;NA;NA;17;30;ns;medium;anc;medium
+19;NA;NA;NA;NA;18;34;ns;medium;anc;medium
+20;NA;NA;NA;NA;19;36;ns;medium;anc;medium
+21;NA;NA;NA;NA;20;37;ns;medium;anc;medium
+22;NA;NA;NA;NA;19;36;ns;medium;anc;medium
+23;po;Anolis pogus;St. Maarten;13.5;2;38;ns;small;small;small
+24;se;Anolis schwartzi;St. Eustasius;14.3;4;38;ns;small;small;small
+25;sc;Anolis schwartzi;St. Christopher;14.3;5;38;ns;small;small;small
+26;sn;Anolis schwartzi;Nevis;14.2;5;38;ns;small;small;small
+27;wb;Anolis wattsii;Barbuda;14.5;6;38;ns;small;small;small
+28;wa;Anolis wattsii;Antigua;14.9;6;38;ns;small;small;small
+29;be;Anolis bimaculatus;St. Eustasius;23.6;10;38;ns;large;large;large
+30;bn;Anolis bimaculatus;Nevis;27.1;11;38;ns;large;large;large
+31;bc;Anolis bimaculatus;St. Christopher;27.9;11;38;ns;large;large;large
+32;lb;Anolis leachi;Barbuda;28.6;12;38;ns;large;large;large
+33;la;Anolis leachi;Antigua;28.8;12;38;ns;large;large;large
+34;nu;Anolis nubilus;Redonda;21.1;13;38;ns;medium;medium;medium
+35;sa;Anolis sabanus;Saba;18.3;14;38;ns;medium;medium;medium
+36;gb;Anolis gingivinus;St. Barthelemy;19.7;15;38;ns;medium;medium;medium
+37;ga;Anolis gingivinus;Antigua;18.8;16;38;ns;medium;medium;medium
+38;gm;Anolis gingivinus;St. Maarten;19.6;16;38;ns;large;large;large
+39;oc;Anolis oculatus;Dominica;22.3;17;38;ns;medium;medium;medium
+40;fe;Anolis ferreus;Marie Galante;28.4;18;38;ns;medium;medium;medium
+41;li;Anolis lividus;Montserrat;18.7;20;38;ns;medium;medium;medium
+42;mg;Anolis marmoratus;Guadeloupe;18.9;21;38;ns;medium;medium;medium
+43;md;Anolis marmoratus;Desirade;19.9;21;38;ns;medium;medium;medium
+44;t1;Anolis terraealtae;Illes de Saintes-1;21.3;22;38;ns;medium;medium;medium
+45;t2;Anolis terraealtae;Illes de Saintes-2;21.5;22;38;ns;medium;medium;medium

examples/bimac.R

@@ -1,5 +1,5 @@
 ## Analysis of Anolis bimaculatus data
-tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species))
+tree <- with(bimac,ouchtree(node,ancestor,time/max(time),spcode))
 plot(tree,node.names=TRUE)
 
 h1 <- brown(log(bimac['size']),tree)
@@ -21,6 +21,7 @@ plot(h4)
 h5 <- hansen(log(bimac['size']),tree,bimac['OU.LP'],sqrt.alpha=1,sigma=1,reltol=1e-5)
 h5 <- update(h5,method='subplex',reltol=1e-11,parscale=c(0.1,0.1),hessian=TRUE)
 h5
+plot(h5)
 
 simdat <- simulate(h5,nsim=10)
 hsim <- update(h5,data=simdat[[1]])

examples/bimac1.R

@@ -1,8 +1,20 @@
 tree <- with(
   bimac,
-  ouchtree(nodes=node,ancestors=ancestor,times=time,labels=species)
+  ouchtree(nodes=node,ancestors=ancestor,times=time,labels=spcode)
 )
 tree
 
 plot(tree)
-plot(tree,node.names=TRUE)
+plot(tree, node.names=TRUE)    # display node names
+
+## When taxon names are long, they are cut off when the
+## default settings are used.  For example:
+tree2 <- with(
+  bimac,
+  ouchtree(nodes=node,ancestors=ancestor,times=time,
+    labels=ifelse(is.na(species),NA,paste(species,island,sep=", "))
+  )
+)
+plot(tree2) # long species names are cut off
+## This is fixed by increasing right margin and font size:
+plot(tree2,margin=0.5)

inst/NEWS

@@ -1,5 +1,10 @@
 _N_e_w_s _f_o_r _P_a_c_k_a_g_e '_o_u_c_h'
 
+_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_6-_6:
+
+        • There is now an example showing how to plot a tree with long
+          taxon names.
+
 _C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_6-_3:
 
         • Error messages and examples have been improved somewhat.

inst/NEWS.Rd

@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for Package 'ouch'}
+\section{Changes in ouch version 2.16-6}{
+  \itemize{
+    \item There is now an example showing how to plot a tree with long taxon names.
+  }
+}
 \section{Changes in ouch version 2.16-3}{
   \itemize{
     \item Error messages and examples have been improved somewhat.